rs3810046

chr18-6941663-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.44 in 232,064 control chromosomes in the GnomAD database, including 24,291 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (15123 hom., cov: 32)
  • Exomes 𝑓: 0.46 (9168 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65530 AN: 151888 Hom.: 15118 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.422

GnomAD4 exome AF: 0.456 AC: 36512 AN: 80058 Hom.: 9168 AF XY: 0.440 AC XY: 18917 AN XY: 42970

Gnomad4 AFR exome AF: 0.341

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.488

Gnomad4 EAS exome AF: 0.203

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.554

Gnomad4 NFE exome AF: 0.532

Gnomad4 OTH exome AF: 0.474

GnomAD4 genome AF: 0.431 AC: 65553 AN: 152006 Hom.: 15123 Cov.: 32 AF XY: 0.424 AC XY: 31481 AN XY: 74270

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.422

Alfa AF: 0.487 Hom.: 21168

Bravo AF: 0.409

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	4.0
Dann	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3810046; hg19: chr18-6941662;